normalizeLoci.SNP {beadarraySNP} | R Documentation

## locus normalization

### Description

Perform locus normalization on Illumina Golden Gate bead arrays

### Usage

       normalizeLoci.SNP(object, method=c("normals","paired","alleles"), NorTum="NorTum",
                         Gender="Gender", Subject="Subject", normalizeTo=2, trig=FALSE)

### Arguments

`object` | `object` class SnpSetIllumina
`method` | character. If `"normals"` then all normal samples in the dataset are used as the invariant set. If `"paired"` then affected samples are normalized to their paired normal samples. `"alleles"` fits a linear model between the B-allele ratio and the signal intensity and normalizes for that
`NorTum` | logical or character vector or name of column in `pData` slot. depicts the normal, unaffected samples in the dataset. In a character vector these should have the value `"N"`
`Gender` | logical or character vector or name of column in `pData` slot. depicts the female samples in the dataset and is used to normalize the sex chromosomes. In a character vector these should have value `"F"`
`Subject` | factor or name of or column in `pData` slot. This factor is used to pair the samples when `method` is `"paired"`
`normalizeTo` | `normalizeTo` numeric. The average copy number of the sample.
`trig` | Logical, use geometric distance of intensity. Otherwise use addition of intensities

### Details

This function is usually performed in the last step of normalization in order to obtain calculated copy numbers.

### Value

This function returns an `SnpSetIllumina` object.

### Author(s)

Jan Oosting

### See Also

`SnpSetIllumina`,`normalizeWithinArrays.SNP`, `normalizeBetweenAlleles.SNP`

### Examples

      data(chr17.260)
      data.nrm<-normalizeLoci.SNP(chr17.260)

[Package beadarraySNP version 1.60.0 Index]